tbuckley/cabot-search huggingface dataset:
Abstract 3413: RTK/SHP2 dependency and feedback adaptation to MEK inhibition defines sensitivity of RAS-mutant proteins to SHP2 inhibitor-based therapies
Authors: Beau Baars, Christos Adamopoulos, Ana Orive-Ramos, Stuart A. Aaronson, Poulikos I. Poulikakos
Journal: Cancer Research (2023)

Abstract Activating RAS mutations constitute the majority of recurrent mutations found in MAPK-driven human tumors. However, RAS mutants have long been considered undruggable, and therefore efforts have been predominantly focused on targeting downstream MAPK signaling. We and others have shown that, MAPK inhibition using MEK inhibitors (MEKi) have limited effectiveness in such tumors due to adaptive resistance. A major mechanism of adaptive resistance involves relief of negative feedback that promotes reactivation of RTK signaling, which in turn activates RAS and results in MAPK rebound. The recent development of direct (i.e. RAS(G12C)) and indirect (i.e. SHP2i, SOSi) inhibitors of RAS have uncovered the dependence of activity of RAS(G12C) and of other RAS mutants on upstream signaling. We and others have previously characterized sensitivity of various RAS mutants in cancer to either SHP2 inhibition (SHP2i), or to combination of SHP2i with MEKi, but a systematic characterization of most RAS mutants commonly expressed in cancer has been lacking. In this study, by combining biochemical and chemical genetic approaches we identified two classes of RAS-mutants, based on their degree of dependency on RTK/SHP2 signaling and adaptation to MEK inhibition. One class of RAS mutants, including most RASQ61X, show complete independence from RTK/SHP2 signaling and are fully resistant to either SHP2i alone or in combination with MEKi. The other class includes the majority of RAS mutants and is characterized by relative resistance to SHP2i, or the combination of SHP2i plus MEKi, compared to cells expressing wild-type RAS, including normal cells. Early clinical data using single agent SHP2i or combinations of SHP2i with MEKi for the treatment of patients with RAS-mutant tumors suggested modest activity as well as dose-limiting on-target (i.e. MAPK pathway related) toxicities. Our findings predict that achieving an acceptable therapeutic index by either approach for treatment of RAS-mutant tumors will be challenging, and they support instead SHP2i-based therapeutic efforts in patients with MAPK-driven tumors expressing wild-type RAS, or in combination with RAS-mutant selective inhibitors. Collectively this work provides a framework for the design of SHP2i-based treatments for patients with MAPK-driven tumors, the majority of which currently have no effective targeted therapeutic options. Citation Format: Beau Baars, Christos Adamopoulos, Ana Orive-Ramos, Stuart A. Aaronson, Poulikos I. Poulikakos. RTK/SHP2 dependency and feedback adaptation to MEK inhibition defines sensitivity of RAS-mutant proteins to SHP2 inhibitor-based therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3413.
Abstract 4288: Predicting DNA methylation in cervical cancer using somatic mutations in a classified mixed model prediction
Authors: Jairo D. Ramos, J. Sunil Rao
Journal: Cancer Research (2023)

Abstract In cervical cancer, the promoter CpG islands of several tumor suppressor genes have been found with abnormal DNA methylation (DNAm) levels, which results in transcriptional silencing. Genetic databases from tumor samples are available without the corresponding DNAm profile. To fulfill this gap and contribute to deciphering the link between genetic variants and DNAm, we performed this study to find a good statistical model for predicting DNAm using genetic data. To address this, we downloaded from the TCGA dataset the genes with significant somatic mutations, as reported by the BROAD Institute, and the DNAm beta values, in known CpG sites, from 307 Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (CESC) samples. Clinical data were also downloaded from patients, including race, age, gender, and cancer stage. We tested five mixed models containing both fixed and random effects to include the unmeasured source of variations in DNAm, for which we used the clustering of samples based on DNAm patterns. Models tested were: Classified mixed model prediction (CMMP), Linear regression model (LM), High dimensional shrinkage estimator based on the elastic net (ENET), a combination of CMMP - ENET, and Random Forest prediction (RF). Besides the significantly mutated genes, the clinical variables were also included as covariates to predict DNAm. We used shared random effects to borrow strength across racial groups, which improves predictive accuracy. Models were enhanced by combining other types of cancers to increase data heterogeneity and the number of samples. Lung Adenocarcinoma (LUAD) and Liver Hepatocellular Carcinoma (LIHC) were selected using Gini and Gap statistics for optimal clustering. Model fitting was evaluated using the average mean squared prediction error (MSPE). Results revealed that the CMMP model with CESC LIHC and LUAD data combined showed the best prediction results (lowest MSPE). The plot of the averaged estimated ENET coefficients indicated that the most important-significantly mutated genes to predict DNAm were CTNNB1, DMD, XIRP2, and PIK3CA. SNPs in these genes linked to cervical cancer include rs121913396, rs121913403 (CTNNB1), rs867262025, and rs121913279 (PIK3CA).In summary, we developed a mixed-effects model for accurately predicting DNAm levels in cervical cancer, using genes with significant somatic mutations (SNVs and INDELs). These results also align with growing evidence suggesting that genetic variation plays a role in DNAm. Citation Format: Jairo D. Ramos, J. Sunil Rao. Predicting DNA methylation in cervical cancer using somatic mutations in a classified mixed model prediction. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4288.
Abstract 1937: Racial differences of epigenome in normal breast tissue reveal biological pathways implicated in racial disparities in breast cancer
Authors: Nan Lin, James Castle, Jinpeng Liu, Chunyan He
Journal: Cancer Research (2023)

Abstract Racial disparity in breast cancer is well recognized. Compared to European American (EA) women, African American (AA) women are more often diagnosed with breast cancer at younger ages, have a more advanced or aggressive disease, and have poorer outcomes. Increasing evidence suggests that biological differences between EA and AA women, particularly differences in epigenetic changes of DNA methylation (DNAm), may contribute to the observed cancer disparity. We hypothesize that racial differences in DNAm in normal breast tissue may reflect distinct genomic susceptibility to breast cancer in different racial groups. Therefore, we investigated epigenome-wide differences of DNAm in normal breast tissue between 178 EA and 272 AA women using the Illumina TruSeq Methyl Capture EPIC library and NGS technology. We identified 17,340 differentially methylated CpG loci (DMLs) between EA and AA women, of which 7,744 were hypermethylated in AA women and 9,596 were hypermethylated in EA women. Pathway analyses of genes annotated to these racial DMLs suggested enrichment of biological processes including cell movement, cell motility, and cell migration, features that are likely linked to the aggressiveness and metastatic potentials of tumor cells. We further examined racial differences in DNAm of breast cancer-related candidate genes and GWAS-identified breast cancer risk loci. Approximately 30% of candidate genes were found to have racial differences in DNAm at more than three CpG sites and these candidate genes were enriched for pathways related to response to stimulus and anatomic structure development. Most interestingly, racial DMLs were found to be enriched for breast cancer risk loci that are associated with risk of estrogen-receptor negative (ER-) breast cancer, treatment response to aromatase inhibitor, and breast cancer-specific morality, phenotypes of which we observed differences between EA and AA breast cancer patients. Our results suggest that racial differences in DNAm in normal breast tissue may induce different biological processes that lead to distinct clinical features of breast tumors observed in EA and AA women and provide an epigenetic mechanism underlying the observed racial disparities. Further research is need to validate the findings of this study. Citation Format: Nan Lin, James Castle, Jinpeng Liu, Chunyan He. Racial differences of epigenome in normal breast tissue reveal biological pathways implicated in racial disparities in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1937.
Abstract 2783: TET2-STAT3-CXCL5 nexus promotes triglyceride transfer from neutrophils to cancer cells to fuel lung adeno-to-squamous transdifferentiation
Authors: Yun Xue, Yuting Chen, Sijia Sun, Hongbin Ji
Journal: Cancer Research (2023)

Abstract Phenotypic plasticity is a rising cancer hallmark and lung adeno-to-squamous transdifferentiation (AST) triggered by LKB1 inactivation is significantly associated with drug resistance. Mechanistic insights into AST are urgently needed to identify therapeutic vulnerability in LKB1-deficient lung cancer. Here we find that Ten-Eleven Translocation (TET)-mediated active DNA demethylation is elevated during AST in KrasLSL-G12D/+;Lkb1L/L(KL) mice, and knockout of individual Tet gene reveals that Tet2 is required for squamous transdifferentiation. STAT3 recruits TET2 to CXCL5 promoter region for demethylation and promotes neutrophil infiltration. Targeting the STAT3-CXCL5 nexus effectively inhibits squamous transdifferentiation through reducing neutrophil infiltration. Interestingly, tumor-infiltrating neutrophil is laden with triglycerides and transfer lipid to tumor cells to promote cell proliferation and squamous transdifferentiation. Pharmacological inhibition of macropinocytosis dramatically inhibits neutrophil-to-cancer cell lipid transfer and blocks squamous transdifferentiation. These data uncover an epigenetic mechanism orchestrating phenotypic plasticity through regulating immune microenvironment and metabolic communication, and identify therapeutic strategies to inhibit AST. Citation Format: Yun Xue, Yuting Chen, Sijia Sun, Hongbin Ji. TET2-STAT3-CXCL5 nexus promotes triglyceride transfer from neutrophils to cancer cells to fuel lung adeno-to-squamous transdifferentiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2783.
Abstract 4279: Method for identifying microsatellite instability high DNA abnormality samples
Authors: Dilmi Perera, Sahand Khakabi, Ka Mun Nip, Sonal Brahmbatt, Adrian Kense, Kevin Tam, David Mulder, Melissa McConechy, David Huntsman, Ruth Miller, Rosalía Aguirre-Hernández
Journal: Cancer Research (2023)

Abstract Introduction: Tissue samples with high microsatellite instability (MSI-H) can be indicators of cancerous tumors that are sensitive to certain types of cancer treatments (e.g., immune modulation-checkpoint inhibitor treatment). MSI-H regions can be identified with Polymerase Chain Reaction (PCR) based assays and next-generation sequencing (NGS). However, these MS regions are susceptible to PCR and sequencing errors. We developed a computational method for detecting microsatellite instability high (MSI-H) tumors using next-generation sequencing (NGS) data to accurately identify true MSI-H samples from MS-Stable samples based on an analysis of these MS regions. Methods: We developed a method for classifying a tissue sample as being microsatellite instability high (MSI-H) without using normal tissue from the same person which doubles the sequencing cost. Furthermore, the algorithm was designed for amplicon targeted assays where it is not always feasible to choose the most predictive MS sites. The machine learning classifier (ML) algorithm is a random forest algorithm with a training set of known MSI-H and MS-Stable samples to learn the relationship between the MSI status and the distribution of repeats in microsatellite regions of genomes using 21 MS loci. A negative control was used to normalize the ML features and therefore reduce the effects of PCR and sequencing errors in noisy MS sites. Results: The MSI detection algorithm was validated in analytical and clinical samples achieving an accuracy greater than 98%. Analytical samples consist of commercial reference standard samples and well characterized FFPE treated cell-lines. Clinical samples consists of clinical FFPE tumor samples from cancer patients that were orthogonally validated using immunohistochemistry (expression of mismatch repair genes, i.e., MMRnormal vs MMRd) on tumor tissue and/or the Promega MSI PCR using matched tumor/normal. All experiments were performed in the Imagia Canexia Health CAP, CLIA, DAP certified laboratory using the Find It assay standard operating procedures for detecting genomic mutations in solid tumor tissue. Conclusions: The MSI detection algorithm can accurately identify samples with MSI-H tumors. When used in a clinical setting, these patients can then be directed to treatments such as immune-checkpoint inhibitors. Citation Format: Dilmi Perera, Sahand Khakabi, Ka Mun Nip, Sonal Brahmbatt, Adrian Kense, Kevin Tam, David Mulder, Melissa McConechy, David Huntsman, Ruth Miller, Rosalía Aguirre-Hernández. Method for identifying microsatellite instability high DNA abnormality samples. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4279.
Abstract 3451: XS-04: A first-in-class dual IRAK4/BTK inhibitor for the treatment of hematological malignancies
Authors: Chunyan Zhao, Jianfei Wang, Aiguo Liu, Xin Gao, Yanfen Teng, Lei Liu, Yang Zhang, Xiaohong Yu
Journal: Cancer Research (2023)

Abstract Bruton's tyrosine kinase (BTK), a critical mediator of B-cell receptor (BCR) signaling, is a validated therapeutic target found across multiple B-cell cancers. Though initially responding to treatment with a BTK inhibitor, many patients with chronic lymphocytic leukemia (CLL), mantle cell lymphoma (MCL), or Waldenström macroglobulinemia (WM) eventually progressed and clinical responses to BTK inhibitors are often poor in diffuse large B-cell lymphoma (DLBCL) patients. These highlight the need to understand the resistance mechanisms and improve responses to BTK inhibitors. The serine/threonine protein kinase IRAK4 is a key modulator of MYD88, which is found to be mutated in various aggressive B-cell lymphomas, including DLBCL. As BCR signaling and MYD88 signaling converge downstream on NF-kB activation, which plays an essential role in proliferation and survival of lymphoma cells, blockade of the two signaling pathways presents a potential therapeutic strategy. Here, we investigated the pharmacokinetic properties and anti-tumor activity of XS-04, a first-in-class dual inhibitor targeting both IRAK4 and BTK, using preclinical models of DLBCL subtypes, including tumors resistant to BTK inhibitors. XS-04 showed potent inhibition of IRAK4 and BTK kinases, with IC50 values of 0.2 and 2.9 nM, respectively. Favorable pharmacokinetic properties were also seen across multiple non-clinical species. Using in vitro anti-proliferative assays, we found that XS-04 inhibited proliferation of various DLBCL cell lines with IC50s of 30 to 40 nM. Mechanistically, XS-04 suppressed NF-kB activity in DLBCL cells and in vivo xenograft tumors, as indicated by decreased phosphorylation of IkBa. Oral dosing of XS-04 in TMD8 xenograft model led to a dose-dependent inhibition of tumor growth, which was comparable to the inhibition shown by a combination of BTK and IRAK4 inhibitors. In addition, XS-04 treatment resulted in tumor regression in a patient-derived ibrutinib-resistant MCL xenograft model, without significant changes in body weight. XS-04, a first-in-class IRAK4/BTK dual inhibitor, shows broad anti-tumor activity across preclinical models of DLBCL subtypes, including tumors resistant to BTK inhibitors. These results support XS-04 as a therapeutic candidate for the treatment of hematological malignancies. An IND submission is planned for 2023. Citation Format: Chunyan Zhao, Jianfei Wang, Aiguo Liu, Xin Gao, Yanfen Teng, Lei Liu, Yang Zhang, Xiaohong Yu. XS-04: A first-in-class dual IRAK4/BTK inhibitor for the treatment of hematological malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3451.
Abstract 6086: PALB2 germline mutations in a large cohort Middle Eastern breast-ovarian cancer patients
Authors: Rong Bu, Abdul K. Sira, Sandeep Parvathareddy, Kaleem Iqbal, Saud Azam, Zeeshan Qadri, Maha Al-Rasheed, Wael Haqawi, Mark Diaz, Ingrid G. Victoria, Khawla S. Al-Kuraya
Journal: Cancer Research (2023)

Abstract Background: The PALB2 gene encoding protein is involved in the homologous recombination repair pathway and plays an important role in maintaining genomic integrity. PALB2 heterozygous pathological variants (PV) or likely pathogenic variants (LPV) are associated with increased risk of breast and ovarian cancer. However, the prevalence and clinicopathological association of PALB2 germline PV/LPV in Middle Eastern breast and ovarian cancers is not fully identified. Purpose: We retrospectively screened a cohort of 918 cancer patients (791 breast cancer and 127 ovarian cancer) from Saudi Arabia using targeted capture-based next generation sequencing (NGS) method for PALB2 germline variants regardless the family history of these patients or the presence of other hereditary cancer susceptibility genes mutations. Clinicopathological criteria were also fully analyzed. Results: Five heterozygous PVs or LPVs were identified in six cases, accounting for 0.65% (6/918) of entire cohort. Two cases (33.3%) harbored PVs and four cases (66.7%) carried LPVs. Four PVs/LPVs (80%) were frameshift along with one novel splicing LPV (c.2835-1 C&amp;gt;A). One recurrent LPV (c.3425delT) was identified in two cases. All six affected carriers have breast cancer diagnosis with median age of 39.5 years (range 34-49 years). Only two cases (33%) have documented family history of cancer. Breast cancer phenotype was invasive ductal unilateral cancer in all cases with 66.7% of hormone receptor positive and 16% of triple negative tumors. Conclusion: Germline PVs/LPVs in the PALB2 gene were observed in low frequency of 0.65% in Saudi breast and/or ovarian cancer. Our study confirms one recurrent LPV and one novel LPV in Saudi breast cancer patients. Citation Format: Rong Bu, Abdul K. Sira, Sandeep Parvathareddy, Kaleem Iqbal, Saud Azam, Zeeshan Qadri, Maha Al-Rasheed, Wael Haqawi, Mark Diaz, Ingrid G. Victoria, Khawla S. Al-Kuraya. PALB2 germline mutations in a large cohort Middle Eastern breast-ovarian cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6086.
Abstract 3992: Elucidating reciprocal interactions between bone marrow stromal cells and a novel γδ CAR T cell therapy in the context of bone metastatic prostate cancer
Authors: Jeremy S. Frieling, Xiomar Bustos, Ryan T. Bishop, Leticia Tordesillas, Daniel Abate-Daga, Conor C. Lynch
Journal: Cancer Research (2023)

Abstract Bone metastatic castrate resistant prostate cancer (CRPC) generates tumors hallmarked by extensive bone formation due to enhanced mesenchymal stem cell (MSC)-osteoblast differentiation. These lesions are at present incurable and substantially diminish patient quality of life, but exciting preclinical studies by our group have shown that these metastases are highly sensitive to gamma delta (γδ) T cell-based CAR-T therapies. However, the impacts of CAR-T cell therapies on the bone microenvironment are presently unknown. Because MSCs are an important stromal component of the cancer-bone microenvironment with emerging immunoregulatory activities, we have recently focused on characterizing the interactions between γδ CAR-T cells and the MSC compartment and their implications for bone metastatic CRPC. Our data show that: 1) γδ CAR-T cells or conditioned media (CM) did not significantly alter MSC viability, 2) MSCs were robustly chemotactic to CM derived from tumor-activated γδ CAR-T cells, 3) MSCs treated with tumor-activated γδ CAR-T CM showed a significant induction of ICAM-1 (9.12-fold, P=0.00640) compared to controls, 4) ICAM-1 silencing significantly reduced γδ CAR-T educated MSC migratory ability, 5) tumor-activated γδ CAR-T CM differentially regulated key genes involved in MSC-osteoblast differentiation, a finding supported by Alizarin red S staining and alkaline phosphatase functional assays, and 6) tri-cultures of MSCs, CRPC cells, and γδ CAR-T cells demonstrate that MSCs significantly enhanced γδ CAR-T mediated CRPC killing. Taken together, we have shown that γδ CAR-T cells promote MSC recruitment in an ICAM-1 dependent manner, and MSCs enhance γδ CAR-T targeted CRPC killing. Reciprocally, γδ CAR-T can promote MSC commitment to osteoblast lineage without impacting their viability. These data are the first to interrogate how bone stromal components regulate γδ CAR-T mediated killing in the context of bone metastatic CRPC. We are currently investigating the mechanisms underpinning the bi-directional interplay between these cell populations. Citation Format: Jeremy S. Frieling, Xiomar Bustos, Ryan T. Bishop, Leticia Tordesillas, Daniel Abate-Daga, Conor C. Lynch. Elucidating reciprocal interactions between bone marrow stromal cells and a novel γδ CAR T cell therapy in the context of bone metastatic prostate cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3992.